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BET Viewer
Version 1.3
USER MANUAL
Contents
Introduction...................................................................................................................................... 1
Configuration ................................................................................................................................ 3
Working screen ................................................................................................................................ 5
Toolbar............................................................................................................................................. 6
Elements of the toolbar ................................................................................................................. 6
Status bar.......................................................................................................................................... 7
Work sheets...................................................................................................................................... 8
Orthogonal Planes ............................................................................................................................ 8
All Slices......................................................................................................................................... 10
3D View ......................................................................................................................................... 11
Rotation ...................................................................................................................................... 12
Light............................................................................................................................................ 12
Misc............................................................................................................................................ 14
Visibility...................................................................................................................................... 14
Box Cut....................................................................................................................................... 15
Movie ......................................................................................................................................... 16
Max. Intensity Projection ................................................................................................................ 19
Electrode View ............................................................................................................................... 20
Misc............................................................................................................................................ 21
Working with BET Viewer .............................................................................................................. 22
Changing the configuration ............................................................................................................ 22
Loading tomographic solutions....................................................................................................... 22
Changing the active work sheet ...................................................................................................... 22
Changing the visualization mode.................................................................................................... 22
Working with the image ................................................................................................................. 22
How to make a 3D rendering?........................................................................................................ 23
Changing the palette....................................................................................................................... 23
Printing the tomographic solution................................................................................................... 23
How to visualize the electrodes? .................................................................................................... 23
Working with animations ............................................................................................................... 24
Description of comnands................................................................................................................ 25
New Image Configuration (Ctrl-N) .................................................................................................. 25
Edit Image Configuration ................................................................................................................ 25
Open Image Configuration (Ctrl-O) ................................................................................................ 26
Open Atlas ..................................................................................................................................... 26
Open Electrodes File....................................................................................................................... 26
Open Solution (F2) ......................................................................................................................... 26
Open fMRI...................................................................................................................................... 27
Save Solution.................................................................................................................................. 27
Import............................................................................................................................................. 28
Export ............................................................................................................................................. 28
Add Comment ................................................................................................................................ 28
Print Setup ...................................................................................................................................... 29
Print Preview .................................................................................................................................. 29
Toolbar of Print Preview ............................................................................................................. 29
Print (Ctrl-P).................................................................................................................................... 30
Exit ................................................................................................................................................. 31
Copy............................................................................................................................................... 31
Copy To.......................................................................................................................................... 31
Copy Options ................................................................................................................................. 32
Clear all.......................................................................................................................................... 33
Show Maximum (F8)....................................................................................................................... 33
Scale Image .................................................................................................................................... 33
Zoom Image ................................................................................................................................... 34
Scale Solution................................................................................................................................. 35
Change Palette................................................................................................................................ 37
Show time course ........................................................................................................................... 39
Generate Movie.............................................................................................................................. 40
Play Movie ..................................................................................................................................... 40
Next Solution.................................................................................................................................. 41
Previous Solution............................................................................................................................ 41
First Solution................................................................................................................................... 41
Last Solution ................................................................................................................................... 41
Go to Solution ................................................................................................................................ 41
Step in Sequence ............................................................................................................................ 42
Set labels ........................................................................................................................................ 42
Toolbar........................................................................................................................................... 42
Status bar........................................................................................................................................ 43
Atlas information bar ...................................................................................................................... 43
Full Screen...................................................................................................................................... 43
Show orthogonal bars..................................................................................................................... 43
Grid's steps..................................................................................................................................... 43
Show grid ....................................................................................................................................... 44
Show vectors .................................................................................................................................. 44
Show Atlas...................................................................................................................................... 45
Grid/Vector style............................................................................................................................. 46
Atlas settings................................................................................................................................... 46
Plot Maximum in sequence ............................................................................................................ 47
Tomography Mode ......................................................................................................................... 47
Inverse Tomography Mode ............................................................................................................. 49
Map Mode...................................................................................................................................... 50
Image Mode ................................................................................................................................... 51
Black & White Mode ...................................................................................................................... 52
Isocontour Mode ............................................................................................................................ 53
Invert Black & White ...................................................................................................................... 54
Use Maximum ................................................................................................................................ 54
Use Maximum ................................................................................................................................ 54
Invert MPI back. ............................................................................................................................. 54
Slice orientation.............................................................................................................................. 55
Plane in All Slices ........................................................................................................................... 55
All Slices Reference ........................................................................................................................ 55
Contents ......................................................................................................................................... 55
Keyword Search.............................................................................................................................. 55
Using Help ..................................................................................................................................... 56
About ............................................................................................................................................. 56
What's This ? .................................................................................................................................. 56
Clear this ........................................................................................................................................ 56
Show Identifiers .............................................................................................................................. 56
Figures
Figure 1. Location of the grid in the image volume........................................................................... 2
Figure 2. Segmentation of the image................................................................................................. 3
Figure 3. Elements of the main screen of BET Viewer. ...................................................................... 5
Figure 4. BET Viewer toolbar. ........................................................................................................... 6
Figure 5. BET Viewer status bar. ....................................................................................................... 7
Figure 6. Orthogonal Planes work sheet. .......................................................................................... 9
Figure 7. All Slices work sheet. ....................................................................................................... 10
Figure 8. 3D View work sheet. ....................................................................................................... 11
Figure 9. Rotation sheet in 3D Parameters. ..................................................................................... 12
Figure 10. Light sheet in 3D Parameters.......................................................................................... 13
Figure 11. Misc. sheet in 3D Parameters......................................................................................... 14
Figure 12. Visibility sheet in 3D Parameters. .................................................................................. 15
Figure 13. Box cut sheet in 3D Parameters. .................................................................................... 16
Figure 14. Movie sheet in 3D Parameters. ...................................................................................... 18
Figure 15. Max. Intensity Projection work sheet. ............................................................................ 19
Figure 16. Electrode View work sheet............................................................................................. 20
Figure 17. Misc. sheet for Electrode View work sheet ..................................................................... 21
Figure 18. Form for Image Configuration. ....................................................................................... 25
Figure 19. Dialog for Open Solution............................................................................................... 26
Figure 20. Add comments window. ................................................................................................ 28
Figure 21. Printer selection dialog. ................................................................................................. 29
Figure 22. Print preview toolbar. .................................................................................................... 29
Figure 23. Print preview. ................................................................................................................ 30
Figure 24. Printing dialog. .............................................................................................................. 31
Figure 25. Copy to bitmap dialog. .................................................................................................. 32
Figure 26. Selection of background color dialog............................................................................. 32
Figure 27. Scale image window...................................................................................................... 34
Figure 28. Zoom image window..................................................................................................... 35
Figure 29. Scale solution window................................................................................................... 37
Figure 30. Change palette window. ................................................................................................ 38
Figure 31. Play movie window. ...................................................................................................... 40
Figure 32. Go to Solution dialog..................................................................................................... 41
Figure 33. Step in sequence dialog. ................................................................................................ 42
Figure 34. Overlapping of the grid on the tomographic slices......................................................... 44
Figure 35. Overlapping of the vectors on the tomographic slices.................................................... 45
Figure 36. Overlapping of the Atlas on the tomographic slices. ...................................................... 46
Figure 37. Selection of style dialog for grid, vectors and Atlas. ....................................................... 46
Figure 38. Tomographic visualization mode................................................................................... 48
Figure 39. Inverse Tomographic visualization mode....................................................................... 49
Figure 40. Map visualization mode................................................................................................. 50
Figure 41. Image visualization mode. ............................................................................................. 51
Figure 42. Black & White visualization mode................................................................................. 52
Figure 43. Isocontour visualization mode. ...................................................................................... 53
Figure 44. Dialog for Isocontour style. ............................................................................................ 54
Figure 45. Slice orientation dialog. ................................................................................................. 55
Figure 46. Parameters report for the rendering 3D. ......................................................................... 56
Acknowledgements
To Dr. Alan Evans from Montreal Neurological Institute and the International Consortium
for Brain Mapping (ICBM) for the brain average (ICBM 305) , probabilistic images, atlas and
templates used in this product.
Microsoft, Windows, Windows 95 , Windows 98 and Windows NT are registered
trademarks of Microsoft Corporation.
Introduction
Introduction
BET Viewer is a system for displaying and evaluating the results of Brain Electrical Tomography
(BET). Brain Electrical Tomography integrates the functional information provided by the
Electroencephalogram (EEG) or Magnetoencephalogram (MEG) with the anatomical information
provided by Magnetic Resonance Imaging or Computer Assisted Tomography. BET makes it possible
to localize in the brain the sources of physiologic or pathologic actvities, thereby opening new ways
to study normal brain processes such as cognition or abnormal brain processes such as epilepsy.
BET requires a solution for the inverse problem of the EEG. This is the problem of estimating the
intracerebral generators given voltage measurements taken from the scalp. Complex calculations
using the recorded electric activity, the coordinates of the scalp electrodes where the EEG was
recorded and tomographic anatomical information lead to an electrical tomography describing the
distribution of cortical currents that generate the recorded electric activity. This tomographic
solution can then be represented in image form using the BET Viewer.
In order to visualize the solution, the BET Viewer needs to be configured with the current elements
in the solution, the grid used to localize these intracerebral currents, and the anatomical images
needed for visualization. The anatomical images can provide the whole brain or only parts of the
brain (segments).
The grid is built over the whole image volume although only the points that intercept with the
chosen segments are used for the calculation as showed in Figure 1. This segmentation could show
the complete brain or just the gray matter, as illustrated in Figure 2.
The anatomical image can contain several million voxels and the grid is built so that it embraces the
largest number of voxels in the regions of interest for the inverse solution. The resolution and
accuracy of BET depends, among other factors, on the number of points in the grid, although there
are limits to the number of points imposed by the inverse solution. The values for the image voxels
that do not intercept with the grid points are obtained by interpolation.
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Introduction
Figure 1. Location of the grid in the image volume
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Introduction
Figure 2. Segmentation of the image.
The "configuration" for BET is stored in a ASCII file with extension .CFG. The elements are:
The anatomical image which used by BET can be an individual image obtained from Magnetic
Resonance Imaging or Computed Assisted Tomography, an average image across many individuals
or an atlas image.
Configuration
Volume Image
Specifies the full path and name for the files (.VOX
and .HDR) containing the complete three dimensional
anatomical image.
Segmentation Solution
Specifies the full path and name of the files (.SEG and
.HDR) containing the segmentation of the anatomical
image used for constraining the tomography.
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Introduction
Segmentation Brain
Specifies the full path and name of the files (.SEG and
.HDR) containing the segmentation of the anatomical
image used to define the brain.
Grid
Specifies the full path and name of the file (.XYZ)
containing the grid used to calculate the solution.
Top View
Specifies the full path and name of the file (.3D)
containing a 3D rendering of the brain corresponding
to the anatomical image seen from above.
Left View
Specifies the full path and name of the file (.3D)
containing a 3D rendering of the brain corresponding
to the anatomical image seen from the left.
Index
Specifies the full path and name of the file (.IND)
containing indexes to the points of the grid used to
calculate the solution.
Atlas
Specifies the full path and name for the files (.VOX
and .HDR) containing the atlas attached to the
anatomical image.
The anatomical image which used by BET can be an individual image obtained from Magnetic
Resonance Imaging or Computed Assisted Tomography, an average image across many individuals
or an atlas image.
BET Viewer can work in two different execution environments:
•
Stand-alone: the system can load and visualize tomographic solutions already calculated and
stored on disk.
•
Linked to a program for calculating the inverse solution: BET viewer will then be called to
visualize the Brain Electrical Tomography images as they are calculated
BET Viewer provides both 2D and 3D visualization of tomographic solutions, sequences of these
visualizations (like movies), and different tools to explore and measure the Brain Electrical
Tomography.
BET Viewer is a Windows-9x/Windows NT compliant 32-bit application that requires large amounts
of memory. At least 64 Mbytes of RAM is needed for the program to work efficiently. Since the
application is devoted to evaluating color images, a video adapter that allows True Color (24 bits) is
recommended.
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Working screen
Working screen
Once BET has been loaded and initialized, the system's main screen is presented. BET Viewer has 5
work sheets with a menu bar, a toolbar and a status bar common to the 5 sheets although there will
be elements that will be available or not depending of the active work sheet.
Application title including tomographic solution and
active configuration
Toolbar
Horizontal menu
Work sheets
Atlas information bar
Status bar
Figure 3. Elements of the main screen of BET Viewer.
The Atlas information bar will be enabled only if the anatomical image of the active
configuration has an associated atlas or the active configuration includes an atlas.
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Working screen
Toolbar
BET Viewer has a toolbar with buttons for the more frequently used commands.
Figure 4. BET Viewer toolbar.
Elements of the toolbar
Open image configuration
Open tomographic solution
Use grid steps
Show orthogonal bars
Set Tomographic mode
Set Inverse tomographic mode
Set Map mode
Set Image mode
Set Black&White mode
Set Isocontour mode
Show solution maximum
Change palette
Print Preview
Print all work sheets
Zoom image
Show vectors
Scale image
Show previous solution
Show next solution
Show first solution
Show last solution
Scale solution
A detailed explanation of these commands will be given in the following chapters.
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Working screen
Status bar
BET Viewer has a status bar describing in several fields the current state of the active work
sheet and other contextual information.
Active Solution
Sequence
Indicator
Image coordinates
Tomography
value
Talairach
coordinates
Active configuration
Figure 5. BET Viewer status bar.
Pressing the right button of the mouse on the fields of the bar gives further
information:
Active
configuration
Sequence indicator
The active image configuration is described.
Image coordinates
This field describes of the x y z coordinates (BET system) used
by the BET Viewer for the present tomograms.
Talairach
coordinates
This provides the equivalent Talairach coordinates if the
anatomical image of the active image configuration is in
Talairach space.
This field shows which image in a sequence is presently
imaged (see command Go to Solution).
The Talairach coordinates are showed only if the anatomical image of the active
image configuration is in Talairach space.
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Work sheets
Work sheets
BET Viewer has 5 work sheets. When a tomographic solution is loaded the Orthogonal Planes sheet
automatically becomes the active work sheet. Three other sheets are also enabled: All Slices, 3D
View and Maximum Intensity Projection, but these are nor visible unless selected. The Electrode
View sheet is enabled only when an electrode coordinates file is loaded.
The names of the sheets appear on tabs at the upper edge of every sheet (just below the tool bar). To
move from sheet to sheet, click the sheet tabs.
Orthogonal Planes
This work sheet visualizes the tomography in 3 orthogonal planes: axial, coronal and
sagittal. The sheet also provides the values of the active scale and palette, two 3D surface
renderings of the brain showing the views from the top and left, and a control for moving
the cursors that define the planes. The X coordinate defines the sagittal plane, the Y defines
the axial and the Z defines the coronal plane. In the top view of the brain the cursors
corresponding to the sagittal (vertical cursor) and coronal (horizontal cursor) plane are
shown. In the left view of the brain the cursors corresponding to the coronal (vertical
cursor) and axial (horizontal cursor) plane are shown.
The slices to be visualized can be selected by changing the cursor values in the boxes on
the sheet or by dragging the mouse over the 3D views to the desired slice. The orthogonal
slices to the slice where the operating system cursor lies, can be visualized too by pressing
the mouse left button. If the anatomical image is aligned in Talairach space, the Talairach
button is enabled and by pressing it a dialog is presented for selecting cursor coordinates in
Talirach’s system.
In each one of the visualized slices the orientation is indicated in the superior border,
where R indicates right, L left, A anterior and P posterior. The slice orientation can ne
changed with the Slice Orientation command. Aditionally, orthogonal bars (with the option
Show orthogonal bars) can be superimposed over every plane showing the position of the 2
orthogonal planes.
When the mouse is moved over the slices the value and voxel coordinates are indicated in
the status bar.
Depending of the current state of the option Grid's steps the cursors will move from
voxel to voxel (inactive state) or in the grid steps. The tomograms are directly
calculated for slices intercepting the grid or interpolated if the slices are not on the
grid.
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Work sheets
Axial plane
Sagittal plane
Coronal plane
Active
palette and
current scale
values
Figure 6. Orthogonal Planes work sheet.
Pressing the right button of the mouse over an elements of the sheet brings up a local
menu with the commands available for the selected element.
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Work sheets
All Slices
This work sheet shows all the tomographic slices that intercept the grid of the selected
plane. The plane used in this sheet is selected through the command Plane in All Slices in
the View menu. An auxiliary reference window gives a 3D rendering of the brain showing
(by means of a line cursor) the position in the brain of the slice selected by the mouse on
the work sheet. This window also shows the values of the active scale and palette. Dragging
the line cursor in this reference window shows the corresponding slice on the work sheet.
The presence on screen of the auxiliary reference window can be controlled with the
command All Slices Reference of the View menu.
In each one of the visualized slices the orientation is pointed out in the superior border,
where R indicates right, L left, A anterior and P posterior.
When the mouse is moved over the slices the voxel coordinates are indicated in the status
bar. The value for each voxel is not shown in this work sheet.
When pressing the right button of the mouse over the elements of the sheet a local
menu is showed with commands available to these elements .
Auxiliary reference window
Figure 7. All Slices work sheet.
The presence on screen of the auxiliary reference window can be controlled with the
command All Slices Reference of the View menu.
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Work sheets
3D View
This work sheet visualizes the tomography in 3 dimensions. The 3D visualization requires
time. Depending on the volume of the image, angles of rotation selected etc., the rendering
can take up to several minutes. When first activated, this sheet appears empty because it
works as a "container " where the renderings will be "stored". An auxiliary window is
attached to this sheet for selecting the different parameters to use in the 3D rendering.
In this sheet is not possible to render the tomography in Black & White and
Isocontour modes.
3D parameters
auxiliary
Figure 8. 3D View work sheet.
The Render button in the auxiliary window called 3D Parameters starts the rendering once
the desired parameters are established. A progress indicator of the rendering then replaces
the status bar. The Cancel button interrupts the rendering at any time.
The rendering process is carried out as a background task so that the user can
continue working with other components of the BET Viewer. The system will notify
the user if he or she tries to execute an operation that would invalidate the
rendering..
Pressing the right button of the mouse over an element of the work sheet brings up a
local menu with commands available to the selected element.
The sheets composing the 3D Parameters window are described next::
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Work sheets
Rotation
In this sheet the rotation angles for the 3D rendering are set.
Angles
There are two ways for setting the angles: by directly editing the desired value
in box existent for each angle or by means of the 6 buttons which can increase
or decrease the rotation angle in steps of 5 . A preview of the sheet shows the
results of applying the active values of the angles for each axis using a model
human head.
Angles edition
Buttons for editing
angles
Preliminary view
Figure 9. Rotation sheet in 3D Parameters.
This sheet shows the position of the image relative to the BET coordinate system.
When the rotation angles are 0 the head looks directly at the observer.
Light
This sheet sets the illumination parameters for the 3D rendering. There are three parameters
for controlling the rendering illumination: position of the light, light intensity and amount of
reflection.
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Work sheets
Buttons for editing
position
Position
coordinates
edition
Intensity
coefficien
Reflection
coefficient
Preliminary view
Figure 10. Light sheet in 3D Parameters.
Position
The position of the light indicated through the coordinates X, Y, Z can
be set by directly editing the values for each coordinate or by pressing
the 6 buttons that increase or decrease the coordinate for each axis in
steps of 5. The default initial position of the light is (0,0,-1) meaning
that the light points to the front of the head.
Intensity
The intensity is a real value between 0.0 and 1.0. The rendering process
combines this coefficient with other factors to achieve the depth effect.
An intensity coefficient of 0.0 ignores the incident light, whereas an
intensity coefficient of 1.0 ignores all other factors. The default initial
value is of 0.5.
Reflection
The reflection coefficient is an integer value between 1 and 10 that
controls the amount of reflection of light from the 3D surface. Higher
values cause highlights and give a metallic appearance to the surface
The Default button allows restoring the implicit values for each parameter. In the preview
of the sheet the result of applying the active values for each parameter is shown with a
model human head.
The default illumination parameters lead to reasonable renderings. These parameters
should be changed only if some unusual illumination is wanted.
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Work sheets
Misc.
This sheet sets two other two parameters for the 3D rendering.
Thresholds
This parameter sets the detection thresholds in the anatomical image of
the skin and the cerebral cortex. These values can be changed using the
edit box existent for each surface. There is no need to change the
default values unless the user wants to "experiment". Wrong values can
invalidate the surface detection process. The Default button allows
restoring the default values for each surface.
Background
This parameter sets the background color of the 3D rendering. The
default initial value is Black.
Background color
selection
Detection thresholds
selection
Figure 11. Misc. sheet in 3D Parameters.
Visibility
This sheet varies the visibility of the cerebral cortex in the 3D rendering. With this
parameter it is possible to reduce the rendering time by inhibiting the rendering in the part
of the head that does not correspond to the brain. To set this parameter the following
controls are used:
All Cortex
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If this toggle is turned on all the brain is visible and the other controls
are disabled.
User Manual, BET Viewer , Version 1.3
Work sheets
Y
This parameter can be directly edited or controlled with the scroll bar.
The brain will be visible at vertical values above the selected Y
coordinate.
The left view of the anatomical image shows the visibility achieved if the current value of
the parameter is applied.
Left image view
Y coordinate
edition
Visibility toggle for
cortex
Figure 12. Visibility sheet in 3D Parameters.
Box Cut
This sheet sets the parameters for cutting out a cubic box from the 3D rendering of the
image. Activating this parameter makes it possible to see into the interior of the image
volume. The controls on the sheet indicate if the option is applied as well as the position
and size of the cube to extract.
Apply Box Cut
Activating option box turns on the cutting algorithm and enables the
other controls.
Position
These parameters set the position of the left inferior corner of the
cube. The 3 controls, one for each coordinate, are controlled by
either an edit box or a scroll bar.
Size
This parameter sets the size of the cube is set. The 3 controls, one for
each coordinate, are cotrolled by either an edit box or a scroll bar.
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Work sheets
The preview superimposes on a model human head the position and size of the extracted
cube (in red) relative to the cube that represents the full image volume (in white). The
coordinates axes are indicated in blue.
Box cut toggle
Position coordinates
edition
Cube size edition
Preliminary view
Figure 13. Box cut sheet in 3D Parameters.
The preview shows the position of the image volume relative to the active rotation
angles. When the rotation angles are 0 the head is looking directly at the observer.
The parameters shown in the figure would extract a cube corresponding to the right
posterior area of the image volume.
Movie
This sheet sets the parameters for carrying out a 3D animation. The resulting animation is
stored in standard Windows format .AVI.
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Generate
movie
If this option is turned on a 3D animation will be generated instead of a
single view when pressing the Render button. Otherwise the remaining
other will be disabled.
Starting from
current
parameters
When this option is activated, the animation (depending on the type of
animation) will begin from the active values of the 3D parameters already
set (Rotation, Light, Box Cut, etc.).
Movie type
Select the animation type from an option list:
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Work sheets
Spins …
This type of animation generates rotations of the image
volume around one of the 3 possible axes. When selected,
the edit box Step is enabled. As many frames as needed
will be generated to complete a full rotation of 360 °
around the selected axis using the selected step.
Cortex
visibility
This type of animation generates views of the image volume
with increasing or decreasing visibility of the cerebral
cortex. When selected, the edit boxes Step and Limit are
enabled. As many frames as needed will be generated to
arrive at the selected limit taking into account the selected
step. The step sign determines if the visibility increases or
decreases (see Visibility sheet).
User
defined
This type of animation generates animations defined by the
user. When selected, a dialog is presented for loading the
file that contains the animation definition. These files have
extension .MUS. Once loaded the file'ss name is shown in
the Input file box.
This type of animation generates temporal animations in 3D
if the active tomographic solution is a sequence. When
selected two edit boxes Start and Stop are shown for setting
the solutions that will be used as start and stop frames in the
movie respectively. This type is visible only if if the active
tomographic solution is a sequence.
Sequence
Format of the .MUS files
The file will have as many lines as frames in the animation. Each line has
the following format:
AX AY AZ YV AppC XPC YPC ZPC XSC YSC ZSC XL YL ZL I R
where:
AX
Rotation angle on the axis X
AY
Rotation angle on the axis Y
AZ
Rotation angle on the axis Z
YV
Coordinate Y for visibility
AppC
1 if Box Cut is carried out, 0 if not
XPC
X coordinate for positioning the Box Cut
YPC
Y coordinate for positioning the Box Cut
ZPC
Z coordinate for positioning the Box Cut
XSC
Size in X axis of the Box Cut
YSC
Size in Y axis of the Box Cut
ZSC
Size in Z axis of the Box Cut
XL
X coordinate for positioning the light
YL
Y coordinate for positioning the light
ZL
Z coordinate for positioning the light
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Work sheets
I
Intensity coefficient of the light
R
Reflection coefficient of the light
Once the Render button is pressed a dialog window requests a filename for the animation
that will be generated in .AVI format. The chosen name will appear in the Output file box.
During the animation, the number of frames rendered will be monitored in the Frames
rendered box.
Toggle for generating
movie
Toggle for using current
parameters
Movie type
selection
Movie type
parameters
AVI file for storing
the movie
Figure 14. Movie sheet in 3D Parameters.
The progress bar of the animation that replaces the status bar during the rendering
shows the progress of each frame separately (and not the progress of the whole
animation process).
The animation can be played with any multimedia player supporting the .AVI format
or with the command Play Movie.
If the Cancel button is pressed during the generation of the animation sequence the
user can save the frames generated until that moment.
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Work sheets
Max. Intensity Projection
Like the Orthogonal Planes sheet this work sheet shows the tomography in 3 orthogonal
planes. All the slices of each plane are projected together onto one slice. If the anatomical
image has a template for this purpose, this is used; otherwise the projection is carried out
onto the middle slice in each plane.
The projection shows at each point of the slice the maximum intensity of all slices in that
plane (see use Maximum). The view is similar to what would be seen if the active areas
were in a "glass head." The sheet also shows the values of the active scale and palette.
In this sheet it is possible to visualize the tomography in either Map or Black & White
modes.
Figure 15. Max. Intensity Projection work sheet.
When moving the mouse cursor over the slices the coordinates are only fully
reported in the status bar if the current voxels intercept the grid. Otherwise only the
two coordinates that intercept the plane are reported.
In this work sheet the command Show vectors is disabled. The command Show grid
is disabled if the projection is carried out over a template associated with the
anatomical image.
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Work sheets
Electrode View
This work sheet shows the electrode positions on the 3 dimensional anatomical image. The
sheet behaves in the same way as the 3D View sheet and there is a similar auxiliary
window for selecting the different parameters to use in the 3D rendering.
3D Parameters auxiliary
window
Figure 16. Electrode View work sheet.
In the auxiliary window the Render button starts the rendering once the desired parameters
have been set. The Cancel button, which is enabled when the rendering begins, allows the
rendering to be interrupted at any time. A progress indicator replaces the status bar. This
progress is divided in two parts: anatomical image rendering and electrode rendering.
This sheet is enabled when loading a file of electrode coordinates with the command
Open Electrodes File. Pressing the right button of the mouse over any element of the
sheet brings up a local menu with commands available to this element.
The rendering process is carried out as a background task, allowingthe user to
continue working with BET Viewer. The user is notified if he or she tries to execute
any operation that could invalidate the rendering.
The 3D Parameters window which sets the parameters for the rendering has 3 sheets: Rotation, Light
and Misc. The Rotation and Light sheets have the same function as those already described in the
3D Parameters window of the work sheet 3D View. The sheet Misc. adds further parameters:
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Work sheets
Misc.
In this sheet the following parameters are set for the 3D rendering.
Thresholds
This parameter sets the detection thresholds in the anatomical image of
the skin and the cerebral cortex. These values can be changed using the
edit box existent for each surface. There is no need to change the
default values unless the user wants to "experiment". Wrong values can
invalidate the surface detection process. The Default button allows
restoring the default values for each surface.
Background
This parameter sets the background color of the 3D rendering. The
default initial value is Black.
Electrode Color
This button changes the color used for rendering the electrodes. When
pressed opens the Windows standard dialog for selecting colors.
Show Identifier
If this toggle is turned on the rendering will include the electrode name
and the Font button will be enabled to allow a standard Windows
standard dialog to select the font.
Skin detection
threshold selection
Background color
selection
Electrode color
selection
Toggle for identifying
electrodes
Font identifier selection
Figure 17. Misc. sheet for Electrode View work sheet
.
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Working with BET Viewer
Working with BET Viewer
Once it has been loaded and initialized, the BET Viewer is ready to start the working session. At the
beginning of the working session, only the Orthogonal Planes sheet will be enabled. The remaining
sheets will be enabled once a tomographic solution is loaded.
The loading and initializations is a slow process which, depending on the power and
memory capacity of the computer, can take up to several minutes.
Changing the configuration
During the working session the configuration can be handled with several commands. With
the commands Edit Image Configuration and New Image Configuration the user can
change the configuration or create a new one. The command Open Image Configuration
allows the user to select and load a stored configuration.
Loading tomographic solutions
If the application is working in stand-alone mode, the tomographic solutions are loaded by
means of the command Open Solution. If the application is executed from another module,
the tomographic solution is loaded automatically when giving the corresponding command
in that module. The loaded solution becomes the active solution and once loaded, the
remaining work sheets are enabled.
Changing the active work sheet
The active work sheet is changed by clicking the sheet tab for the desired sheet. The
selected sheet will then become the active work sheet.
Changing the visualization mode
BET Viewer has five visualization modes: Tomographic, Inverse Tomographic, Image, Map,
Black & White and Isocontour. To change the mode use the commands Tomography Mode,
Inverse Tomography Mode, Image Mode, Map Mode, Black & White Mode and Isocontour
which appear in the toolbar or the View menu. The selected mode will become the active
visualization mode.
Working with the image
In the sheets Orthogonal Planes, All Slices and Max. Intensity Projection the tomographic
solution is visualized in 2D by means tomographic slices. The tomographic solution is
visualized in each work sheet using the active visualization mode as well as the active
solution and image scale. To change the solution scale use the command Scale Solution
and for changing the image scale the Scale Image will be used.
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Working with BET Viewer
How to make a 3D rendering?
To obtain a 3D rendering of the tomographic solution, activate the 3D View work sheet (see
3D View). The minimum steps needed to achieve a rendering are:
•
Set the rotation angles. Activate the Rotation sheet of the 3D Parameters window and
using the preview put the volume in the desired position (see Rotation).
•
Set the visibility of the brain cortex. Activate the Visibility sheet of the 3D Parameters
window and using the preview set the visibility of the cortex in the desired position (see
Visibility).
•
To see the interior of the image volume activate the Box Cut sheet of the 3D Parameters
window and using the preview set the size and position of the cube to extract (see Box
Cut). If not desired, pass on to the next step.
•
Press the Render button in the 3D Parameters window to start the rendering process.
This process is carried out as a background task allowing the user to continue with
other tasks.
Changing the palette
BET Viewer is distributed with a set of color palettes for visualizng the tomographic
solution. The selected palette will be used in all the work sheets except the Black&White
mode. When beginning a new working session the last used palette will be selected. To
change the palette the command Change Palette will be used.
Printing the tomographic solution
BET Viewer can print the contents of the different work sheets. The Print Setup command
configures the printer and selects the pages to print. The Print command prints the selected
sheets. The Add Comment command adds comments or observations to the work sheets for
printing. The Print Preview command previews the sheets as they will appear on paper.
How to visualize the electrodes?
To obtain a 3D rendering of the electrodes requires loading the file of electrode coordinates
by means of the Open Electrodes File. Inmediately after 5 renderings are generated
automatically corresponding to the front, back, top, left and right views of the head. To
obtain a different view the minimum steps needed to achieve it are:
•
Activate the Electrode View work sheet (see Electrode View)
•
Set the rotation angles. Activate the Rotation sheet of the 3D Parameters window and
using the preview put the volume in the desired position (see Rotation).
•
To change any of the default values for rendering the electrodes, activate the Misc.
sheet and change the desired parameter (see Misc. in Electrode View).
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Working with BET Viewer
•
Press the Render button in the 3D Parameters window to start the rendering process.
This process is carried out as a background task so that the user can continue with other
tasks.
Working with animations
There are two animation (movies) types in BET Viewer:
•
Temporal animation using the command Generate Movie in the Display menu, or by
using the the Movie sheet of the Parameters 3D in the work sheet 3D View with the
movie type Sequence.
•
3D animation using the Movie sheet of the Parameters 3D in the work sheet 3D View
The temporal animation with Generate Movie is only enabled when working with a
sequence of solutions. In both types the animation generated is saved in .AVI format
allowing it to be used with any multimedia player or with the command Play Movie in the
Display menu.
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Description of comnands
Description of comnands
This section descirbes all the commands, specifying for each the menu where it belongs, the hot-key
combination (if available), and the toolbar button (if it exists).
New Image Configuration (Ctrl-N)
This command in the File menu creats a new configuration (see Configuration). When
activated, a form for changing the elements of the configuration appears. The elements that
appear when the form is presented correspond to the active configuration. Pressing the Ok
button brings up a dialog window for saving the configuration.
Figure 18. Form for Image Configuration.
Edit Image Configuration
This command in the File menu allows editing an existent configuration (see Configuration).
When activated, a dialog for selecting the configuration to be edited appears. Once the
configuration is loaded, a form for editing the elements of the configuration appears.
Pressing the Ok button brings up a dialog window for saving the configuration.
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Description of comnands
Open Image Configuration (Ctrl-O)
This command in the File menu allows loading an image configuration (see Configuration).
When activated, a dialog for selecting the desired configuration appears. Once the
configuration is selected, the loading and reinitialization process starts.
When a new configuration is loaded all the work sheets are reinitialized, and the
previous contents of the work sheets are lost.
Open Atlas
This command in the File menu loads an atlas file for viewing over the anatomical image in
the active configuration (see Show Atlas). When activated a dialog for selecting the desired
atlas file is presented.
Open Electrodes File
This command in the File menu loads a file of electrode coordinates for later visualization
on the anatomical image. When activated, a dialog for selecting the desired file appears
and inmediately after 5 renderings are generated automatically corresponding to the front,
back, top, left and right views of the head.
When a new file of electrode coordinates is loaded the work sheet Electrode View is
enabled or reinitialized (thus losing its previous contents).
Open Solution (F2)
This command in the File menu loads a tomographic solution. When activated, a dialog for
selecting the desired solution appears.
Solution
type
selection
Figure 19. Dialog for Open Solution.
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Description of comnands
There are five possible solution types: .TXT, .ENG, .ORT, .MDL and .MOD. The .TXT and
.ENG files are ASCII files, the .ORT and .MDL files are binary files storing floating point
numbers in single precision (4 bytes).
The .TXT and .ORT files include information about the orientation and magnitude of the
generators. The .ENG and .MDL files only include information about the magnitude. The
solution files can contain a single solution or a sequence of them. There are specific
commands for working with a sequence of solutions.
The .MOD files, correspond to the models obtained for the electrical tomography by the
Quantitative Analysis of the EEG (frequency domain).
Open fMRI
This command in the File menu loads a fMRI file. When activated, a submenu appears for
selecting which variant will be used for loading the fMRI file: Individual or Atlas. When the
Individual option is selected a dialog is presented for setting the elements needed for fMRI
visualization.
The anatomical images can be in VOX or ANALYZE format. The fMRI files are loaded only
in ANALYZE format. The Segmentation file is optional, if no file is set, the segmentation is
generated automatically by the system. However is recommened to set a segmentation file
as precise as possible in order to obtain better results in visualization. The grid step by
default is 3 and can be changed by the user in order to increase accuracy in the
visualization. It is user’s responsibility to guarantee coregistring between the anatomical
image and the fMRI file.
When the Atlas option is selected a dialog is presented for selecting the fMRI file to load. In
this option the fMRI is plotted over the ICBM brain template requiring in this case a
previous normalization and coregistering with this brain.
Save Solution
This command in the File menu saves a tomographic solution. When activated, a dialog for
editing the name for the solution to be saved appears. If the active solution includes
information about the orientation of the generators (.TXT, .ORT) it is possible to save it
without that information by selecting the .ENG or .MDL type in the dialog.
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Description of comnands
Import
This command in the File menu imports an image volume in ANALYZE ™ format or iMagic
format as a tomographic solution. When activated, a dialog for selecting the desired image
appears. If the image to be imported contains more than one volume the generated solution
will be considered a sequence.
Only the ANALYZE ™ images stored in transverse orientation (axial) can be
imported.
To be imported the image dimensions should match with the anatomical image
dimensions or grid dimensions of the active configuration.
Export
This command in the File menu exports a tomographic solution (or a sequence of them) to
an image in ANALYZE ™ format or iMagic format. When activated, a dialog for editing the
name for the solution to be exported appears. The dialog allows to select the image type to
export for the ANALYZE format: grid image or full image. If the grid image type is selected
only the solutuion values matching with the grid will be exported, obtaining in this way a
more compact and reduced in size image. The full image type saves all the image values.
Add Comment
This command in the File menu adds comments to the sheets for printing. When activated,
a window for editing the desired text appears. In the window there is an option list (In Page)
for selecting the sheet where the comment will appear. The comment added using the All
option appears in all the sheets before the comment specific to the particular sheet.
Page selection
Figure 20. Add comments window.
The comments will appear on the printed page after the content of the sheet.
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Description of comnands
Print Setup
This command in the File menu sets the characteristics of the printer. When activated, a
dialog that also sets the paper size and orientation appears.
Figure 21. Printer selection dialog.
It should be kept in mind when selecting the paper size that some sizes are not valid
for printing in BET Viewer.
Print Preview
This command in the File menu replaces the main window of the application for a window
where a preview shows the work sheets as they would look on paper when printed. The
window has a toolbar with commands for adjusting the preview.
Toolbar of Print Preview
Previous page
One page
activation
Next page
Two pages
activation
Current page(s)
indicator
Zomm % selection
Full screen
activation
Print all pages
Close preview
Figure 22. Print preview toolbar.
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Description of comnands
Toolbar
Page header
Comments added
to the page
Figure 23. Print preview.
The work sheets Orthogonal Planes and Max. Intensity Projection are printed in a single
page respectively but the remaining sheets can take more than a page depending on their
contents. The work sheets Orthogonal Planes and Max. Intensity Projection are therefore
numbered 1 and 2. The work sheet All Slices will start on page 3 and will use as many
pages as needed. The numbering will then continue with the work sheets 3D View and
Electrode View.
Depending on the form of the mouse cursor:
or
, when pressing the left
button of the mouse the magnification of the page will be increased or reduced.
In the page headers the following elements appear: application logo, center where BET
Viewer is installed, company (or distributor) logo, active tomographic solution, active
configuration and page number.
Print (Ctrl-P)
This command in the File menu prints of the BET Viewer work sheets (see Print Preview).
When activated, a dialog is shown for setting the characteristics of the printer and the pages
to print. When the Ok button is pressed the printing starts.
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Description of comnands
Figure 24. Printing dialog.
Exit
This command in the File menu allows leaving the application after confirmation.
When BET Viewer is executed through a linked system, special attention should be
paid when closing the application because undesired effects can be caused in the
linked system. It is therefore recommended that the BET Viewer be closed prior to
returning to the linked system.
Copy
This command in the Edit menu copies the contents of the active work sheet to the
Windows clipboard.
This command is only enabled if the active work sheet has content.
Copy To
This command in the Edit menu allows copying the content of the active work sheet to a
Windows bitmap file. When activated a dialog for selecting the name of the file appears.
The dialog also shows the existent files on disk.
Preliminary view
in real size
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Description of comnands
Preliminary
view
Bitmap type selection
Figure 25. Copy to bitmap dialog.
This command is only enabled if the active work sheet has content.
Copy Options
This command in the Edit menu sets the background color of the bitmaps saved with the
commands Copy or Copy To. When activated, a dialog for setting the 3 possible
background colors appears.
Figure 26. Selection of background color dialog.
The selection made with this command is also used for the bitmaps used in the
animations generated by the command Generate Movie.
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Description of comnands
Clear all
This command in the Edit menu erases all the renderings that have been carried out in the
work sheets 3D View and Electrode View.
This command is only enabled when there is at least one rendering. For erasing only
one of the renderings the command Clear this should be used instead of Clear all.
Show Maximum (F8)
This command in the Display menu makes the work sheet Orthogonal Planes show the 3
planes containing the point where the tomographic solution reaches its maximum
magnitude (see Use Maximum)
This command is only enabled in the work sheet Orthogonal Planes.
Scale Image
This command appears in the Display menu and in the local menus of all the work sheets.
By means of this command it is possible to scale the anatomical image to obtain better
contrast for the image. When activated, a window is presented with several controls that
allow carrying out the scaling:
Minimum
This parameter sets the minimum of the scale using either the edit
box or the scroll bar.
Maximum
This parameter sets the maximum of the scale.
Threshold
This parameter, which is only enabled if the active visualization
mode is Black & White, controls the threshold for the imagecontouring operation (see Black & White Mode).
Best Fit
If this toggle is turned on, the parameters Maximum and Minimum
are adjusted automatically using the last slice on which the mouse
cursor was located.
Preview
If this toggle is turned on, the window is enlarged to preview the last
slice on which the mouse cursor was located using the active
parameters for scaling.
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Description of comnands
Mimimum,
Maximum and
Threshold
values edition
Preliminary
view
Figure 27. Scale image window.
This command scales the anatomical image and not the tomographic solution. Use
the command Scale Solution for scaling the solution.
Zoom Image
This command appears in the Display menu and in the local menus of all the work sheets.
This command makes it possible to magnify that part of the image indicated by the mouse
cursor.
When activated, a window is opened for showing with the active zoom factor the area of
the image where the mouse cursor is located. Pressing the left mouse button increases the
zoom factor. If the left button is pressed in combination with any of the Shift keys the zoom
factor is decreased. The zoom factor varies between 2x and 20x.
When this command is activated the form of the mouse cursor changes to
to indicate the direction of the magnification.
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Description of comnands
Current zoom
factor
Zoom window
Figure 28. Zoom image window.
The zoom window stays open until it is explicitly closed by the user.
Scale Solution
This command appears in the Display menu and in the local menus of all
the work sheets. By means of this command is possible to scale the active
tomographic solution. When activated, a window is shown that sets the scale type and its
parameters. There are 8 scale types:
MaxMin
In this scale type the values minimum and maximum for scaling the
tomographic solution are defined. When this type is selected two edit
box are shown: Minimum and Maximum for editing the values. The
toggle Best Fit automatically adjusts the scale based on the extreme
values of the tomographic solution.
Threshold
With this scale type is possible to focus on the positive and negative
values in the tomographic solution. When this type is selected the
edit box Threshold is shown to define the threshold that will be used
as the scale limit in both directions: positive and negative. The toggle
Best Fit automatically adjusts the scale based on the extreme value of
the tomographic solution.
Step
This scale type highlights the peak values inside the tomographic
solution. When this type is selected the edit box Step is shown for
defining the scaling parameter which is a positive value. Bigger
values cause more highlighted peaks. A value of 0 is equivalent to a
Threshold scale with Best Fit turned on.
Pos/Neg Peak
This scale type explicitly visualize the peak positive and negative
values inside the tomographic solution. This effect is achieved by
temporarily zeroing all the values in the tomogram that do not
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Description of comnands
coincide with the peak values. When this scale type is selected, the
edit box Maximum is shown to define the value that will serve as
extreme value in both directions. The toggle Best Fit is also shown
which when turned on automatically adjusts the scale based on the
extreme value of the tomographic solution.
Positive Peak
This scale type explicitly visualize the peak positive and negative
values inside the tomographic solution. This effect is achieved by
temporarily zeroing all the values in the tomogram that do not
coincide with the peak values. When this scale type is selected, the
edit box Maximum is shown to define the value that will serve as
extreme value in both directions. The toggle Best Fit is also shown
which when turned on automatically adjusts the scale based on the
extreme value of the tomographic solution.
Percent
With this scale type it is possible to work with the values of the
tomographic solution in relative rather than real magnitudes.
Conceptually it is similar to the MaxMin type but the values are
scaled by percent. For the percent conversion the maximum value of
the tomographic solution is taken as 100% converting the rest of the
values in relation to the maximum. When this type is selected two
edit boxes are shown: Minimum and Maximum for defining the
values in % and the toggle Best Fit which when turned on causes an
automatic adjustment based on the extreme values of the
tomographic solution.
Peak Percent
This scale type is similar to Percent but here it is possible to
determine the sign of the peak value that will be taken as the
reference of 100%. When this type is selected the edit box Minimum
is shown to define the minimum value in % (the maximum is always
100) as well as a radio control Peak to set the sign of the peak value.
Spot
With this scale type only the values of the tomographic solution
included in the interval defined by the parameters are visualized.
When this type is selected the edit boxes Minimum and Maximum
are shown to define the interval used for scaling. If the minimum and
maximum of the solution are given as parameters then this scale type
is equivalent to a MaxMin scale with Best Fit turned on. Contrasting
with the Maxmin scale type, the values outside the interval are not
plotted.
Spot bipolar
This scale is similar to Spot., only the values of the tomographic
solution included in the interval defined by the parameters are
visualized. When this type is selected the edit boxes Minimum and
Maximum are shown to define the interval used for scaling in the
positive direction. The solution values outside the interval (positive
and negative directions) are not plotted.
The BIPOLAR palette (see Change Palette) is recommended when using the following
scale types: Threshold, Step, Pos/Neg Peak and Positive Peak.
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If the toggle Keep scale parameters is turned on, every time a new tomographic
solution is loaded, it will be scaled using the last scale parameters used. Otherwise
the scale parameters will be adjusted automatically using the extreme values of each
tomographic solution.
Tipo de escala
Parámetros del tipo
de escala
Figure 29. Scale solution window.
The toggle Sequence best fit only appears if the current tomographic solution is a
sequence. When turned on, an automatic fit is done using the extreme values of the
whole sequence and not only the extreme values of the current solution (as the Best
Fit toggle does).
Notice that this command scales the tomographic solution and not the anatomical
image. Use the command Scale Image for the anatomical image.
Change Palette
This command appears in the Display menu and in the local menus of all the work sheets.
Using this command is possible to change the active palette by selecting a new one or by
editing the present one. When this command is activated a window is shown with several
controls: an option list indicating the active palette's name, the active palette's preview, an
option for interpolating the palette and the Edit button for editing the palette.
The palettes in BET Viewer can use up to 256 colors. If the palette does not have 256
colors (as usual) and the option for interpolating is set, the application linearly interpolates
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Description of comnands
the present colors up to 256 to obtain the palette that is actually used in the work sheets. If
the option for interpolating is not set, the palette will be used without interpolation.
By means of the option list it is possible to select any one of the available palettes. Once the
window is closed with the Ok button the newly selected palette will become the active
palette of the application. If the Edit button is pressed the window is enlarged adding new
controls to change the palette.
Palette
selection
Preliminary
view
Interpolation
option
Number of
colors
Current color
Button for
changing color
Buttons for
moving colors
Add and Delete
color buttons
Figure 30. Change palette window.
Button for
editing
palette
The first element that appears is a vertical bar divided by the quantity of real colors that
compose the palette. The colors are denoted in bottom up order from 0 to the number of
colors-1. The number of colors is indicated in the box Colors.. Dragging the mouse over the
cursor ( ) to the right of this bar sets the active color. The active color can also be selected
with the edit box Current.
There are also 5 buttons for editing the palette:
This button changes the active color. When pressed, opens the
standard Windows dialog for selecting colors.
This button moves the active color up in the palette. It is disabled
when the active color is the last one in the palette.
This button allows moving the active color down in the palette. It is
disabled when the active color is the first one in the palette.
This button adds a new color in the palette. When pressed, opens the
standard Windows dialog for selecting colors. Once chosen, the new
color becomes the active color and is inserted after the previously
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Description of comnands
active color. It is disabled when the palette reaches the maximum of
256 allowed colors.
This button erases the palette's active color. The following color
becomes the new active color. This button is disabled when the
palette reaches the minimum of 2 colors.
When pressing the Ok button a dialog for saving the recently edited palette is presented if
any editing was carried out. The palette files are stored as files .LEV in the application's
directory.
The palette GRAYS cannot be altered since it is the one used by the Black & White
visualization mode. The palette BIPOLAR can be edited but should keep its name.
Show time course
This command in the Display menu shows the temporal course (if a sequence is loaded) of
a selected voxel. When activated a dialog is presented containing a plotting window
showing the temporal course of the voxel indicated by the orthogonal cursors in the
Orthogonal Planes sheet.
The dialog can be closed with the Close button at any moment staying visible for allowing
updating of the plotting window with a new voexl whenever the cursor position is changed.
If the cursor position is updated by pressing the Alt key in conjunction with the left button
mouse a new voxel is added to the plotting window instead of updating it.
The vertical bar in the plotting window is a cursor for selecting a temporal point inside the
temporal course. The tomographic solution corresponding to that point is updated in the
working sheets whenever the cursor is updated.
In the dialog other elements are presented. The combo box Voxel allows to select the active
voxel (if more than one is plotted). The voxel visibilty can be set wit the check box besides
the combo box as well as the color and thickness of the wave. The following combo box
shows the current temporal instant as well as the voxel’s value in that temporal position.
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Description of comnands
Generate Movie
This command in the Display menu creates a temporal animation using the sequence
already loaded. When activatated, the command shows a dialog for selecting the filename
for saving the animation in .AVI format. Once the selection is made, the animation begins
starting with the first solution in the sequence and using the active parameters for working
with sequences (see Scale Solution and Step in Sequence).
The animation generated can be played with any multimedia player supporting the
.AVI format or with the command Play Movie.
Movie generation can be aborted by pressing the Esc key.
Play Movie
This command appears in the Display menu. With this command it is possible to play any
.AVI animation created with Generate Movie, with the 3D View work sheet or any other
application. When pressed a dialog is shown for loading the .AVI file desired. Once the file
is loaded a window is shown with 7 buttons: Play, Play, Stop, First frame, Rewind, Fast
forward, Last frame and Close that will control the execution of the animation. There is
also a track bar which monitors the animation status.
Figure 31. Play movie window.
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Description of comnands
Next Solution
This command in the Display menu.loads the tomographic solution following the active
one in the sequence (see Open Solution) taking into account the defined step (see Step in
Sequence). The command is disabled if the active tomographic solution is not a sequence
or if it is the last one in the sequence.
Previous Solution
This command in the Display menu loads the tomographic solution before the active one in
the sequence (see Open Solution) taking into account the defined step (see Step in
Sequence). The command is disabled if the active tomographic solution is not a sequence
or if it is the first one in the sequence.
First Solution
This command in the Display menu loads the first tomographic solution of the sequence
(see Open Solution). The command is disabled if the active tomographic solution is not a
sequence or if the active solution is the first one in the sequence.
Last Solution
This command in the Display menu loads the last tomographic solution of the sequence
(see Open Solution). The command is disabled if the active tomographic solution is not a
sequence or if the active solution is the last one in the sequence.
Go to Solution
This command in the Display menu. selects a particular solution inside the sequence (see
Open Solution). The command is disabled if the active tomographic solution is not a
sequence.
Figure 32. Go to Solution dialog.
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Description of comnands
Step in Sequence
This command in the Display menu setts the step which will be used for moving between
solutions in the sequence. (see Open Solution). The command is disabled if the active
tomographic solution is not a sequence.
Figure 33. Step in sequence dialog.
Set labels
This command in the Display menu allows tu set labels for the current sequence loaded.
When activated a dialog is presented for setting the parameters needed for generating
automatically the sequence labels. There are 3 edit boxes: Initial Value, Sampling rate and
Units. The Initial Value field allows to set by using digits the starting value for the sequence
labels. Sampling rate will indicate the numeric value needed for obtaining the label for the
next labels. The label value in a given instant is calculated by adding the label value in the
previous instant with 1/ Sampling rate. The Units field will indicate the units used if any.
The command is disabled if the active tomographic solution is not a sequence.
Toolbar
This command in the View menu works as a toggle: when turned on the toolbar is
visualized under the horizontal menu of the application; otherwise the toolbar is hidden,
leaving more space on screen for the work sheets.
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Status bar
This command in the View menu works as a toggle: when turned on the status bar is
visualized in the bottom of the main window application; otherwise the status bar is
hidden, leaving more space on screen for the work sheets.
Atlas information bar
This command in the View menu works as a toggle: when turned on the Atlas information
bar is visualized at the bottom of the main window application above the status bar;
otherwise the Atlas information bar is hidden leaving more space on screen for the work
sheets. This bar shows the name of the anatomical structure where the mouse cursor is
located.
This command only is enabled if the anatomical image of the active configuration
has an associated atlas or the active configuration includes an atlas.
Full Screen
This command in the View menu works as a toggle: when turned on the main window
application is maximized and at the same time the horizontal menu, the toolbar, and the
status bar are hidden, leaving the whole available space on screen for the work sheets. Use
the Esc key to return to the normal mode.
Show orthogonal bars
This command in the View menu works as a toggle: when turned on, bars indicating the
position of the 2 orthogonal planes to every plane are shown on it.
This command only is enabled in the work sheet Orthogonal Planes.
Grid's steps
This command in the View menu works as a toggle: when turned on, the cursors of the
sheet Orthogonal Planes will move only in the grid's steps and when turned off they will
move from voxel to voxel. The tomographic values are directly calculated for the slices
intercepting with the grid and interplolated for other slices.
This command only is enabled in the work sheet Orthogonal Planes.
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Show grid
This command in the View menu works as a toggle: when turned on, the grid points are
superimposed on the tomographic slices visualized in the work sheets. The activation of this
command inactivates the command Show vectors and vice versa.
Figure 34. Overlapping of the grid on the tomographic slices.
The overlapping of the grid is not carried out in the 3D View sheet and the command
is disabled in that sheet.
The overlapping of the grid is carried out only over the slices intercepting the grid.
Show vectors
E This command appears in the View menu. It works as a toggle, when turned on, the
vectors which indicate the generators direction are superimposed on the tomographic slices
visualized in the work sheets. The activation of this command inactivates the command
Show grid and viceversa. The vectors are visualized by means of arrows that point in the
corresponding direction of the current dipoles. If the direction is perpendicular to the plane,
it will be indicated with a point or a cross if the vector is "entering" or "leaving" respectively.
Overlapping of the vectors is not carried out in the 3D View or in the Max. Intensity
Projection sheets and the command is disabled in these sheets. If the type of active
tomographic solution does not contain information about the direction of the
generators, e.g. .ENG files, the command is also disabled.
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Overlapping of the vectors is carried out only over the slices intercepting the grid.
Figure 35. Overlapping of the vectors on the tomographic slices.
Show Atlas
This command in the View menu works as a toggle: when turned on, the atlas is
superimposed on the tomographic slices in the work sheets.
The overlapping of the atlas is not carried out in the 3D View or in the Max. Intensity
Projection sheets and the command is disabled in these sheets.
This command is only enabled if the anatomical image of the active configuration
has an associated atlas or the active configuration includes an atlas.
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Figure 36. Overlapping of the Atlas on the tomographic slices.
Grid/Vector style
This command in the View menu brings up a window to define the style for visualizing the
grid (with the command Show grid) and the vectors (with the command Show vectors).
The Complement or Solid style can be selected using the radio control. The style
Complement uses the color complementary to the color already on screen. The style Solid
draws using a specified color. If the Solid style is chosen the Color button is enabled and
pressing it brings up the standard Windows dialog for selecting colors.
Figure 37. Selection of style dialog for grid and vectors.
Atlas settings
This command in the View menu set the atlas configuration for viewing. When activated, a
dialog is presented for setting visibility, color and style for the different structures present in
the atlas.
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Description of comnands
With the Structures list it is possible to select the structure(s) for changing its attributes
(visibility and color). The commands Load and Save allow to load and save respectively
visibility and color settings from/to a ATS file for using them in ulterior working sessions.
Plot Maximum in sequence
This command in the View menu works as a toggle: when turned on, every time a solution
is loaded from the sequence (see Open Solution), the Orthogonal Planes sheet will visualize
the solution in the 3 planes containing the point where the tomographic solution reaches its
maximum magnitude and the solution will be scaled automatically using its extreme values
(see Use Maximum). The command is disabled if the active tomographic solution is not a
sequence.
Tomography Mode
This command in the View menu sets the active visualization mode to tomography. In this
mode the integration of the color of the tomographic solution with the anatomical image is
carried out using the intensity of the anatomical image as the intensity coefficient for the
color. The voxels of the anatomical image with more intensity will have a brighter color in
the tomographic solution. This command is one of several options to set the active
visualization mode: Inverse Tomography Mode, Map Mode, Image Mode and Black&White
Mode.
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Figure 38. Tomographic visualization mode.
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Inverse Tomography Mode
This command in the View menu sets the active visualization mode to inverse tomography.
In this mode the integration of the color of the tomographic solution with the anatomical
image is carried out in the same way as in the Tomographic mode using the intensity of the
anatomical image as intensity coefficient for the color, but the inverse of the intensity of the
anatomical image is used. The voxels of the anatomical image with more intensity will have
a darker color in the tomographic solution and vice versa. This command is one of several
options to set the active visualization mode: Tomography Mode, Map Mode, Image Mode
and Black&White Mode.
Figure 39. Inverse Tomographic visualization mode.
With this mode is possible to highlight the color in the gray matter and to attenuate
the color in the white matter of the brain.
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Map Mode
This command in the View menu sets the Map mode as the active visualization mode. In
this mode there is no integration of the color of the tomographic solution with the
anatomical image. The tomographic solution is visualized independently of the underlying
anatomical image. This command is one of several options to set the active visualization
mode: Tomography Mode, Inverse Tomography Mode, Image Mode and Black&White
Mode.
Figure 40. Map visualization mode.
With the Map mode is possible to visualize details of the tomographic solution that
might be hidden if the solution were integrated with the anatomical image .
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Description of comnands
Image Mode
This command in the View menu sets the Image mode is set as the active visualization
mode. In this mode as in the Map mode there is no integration of the color of the
tomographic solution with the anatomical image. The anatomical image is visualized
ignoring the corresponding tomographic solution. This command is one of several options
to set the active visualization mode: Tomography Mode, Inverse Tomography Mode, Map
Mode and Black&White Mode.
Figure 41. Image visualization mode.
The Image mode is very convenient for visualizing the details of the anatomical
image that could not be easily observed when integrated with the tomographic
solution.
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Black & White Mode
This command in the View menu sets the Black & White mode as the active visualization
mode. In this mode the tomographic solution is visualized with a gray palette (GRAYS) and
the anatomical image is reduced to contours. There is no real integration of the color of the
tomographic solution with the anatomical image. This command is one of several options
to set the active visualization mode: Tomography Mode, Inverse Tomography Mode, Map
Mode and Image Mode.
To control the contouring of the anatomical image the command Scale Image should
be used to vary the Threshold parameter and its relationship with Maximum and
Minimum.
The Black & White mode is very convenient for printing on printers without color
capability.
Since the palette is automatically change in this mode, the palette should be checked
when changing to another visualization mode.
Figure 42. Black & White visualization mode.
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Description of comnands
Isocontour Mode
This command in the View menu View sets the Tomographic mode as the active
visualization mode. In this mode the tomographic solution is visualized through isocontours
that are superimposed on the underlying anatomical image. This command is one of several
options to set the active visualization mode: Tomography Mode, Inverse Tomography
Mode, Map Mode, Image Mode and Black&White Mode.
Figure 43. Isocontour visualization mode.
The command Isocontour style controls how the isocontours cover the image.
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Invert Black & White
This command appears in the View menu. It works as a toggle to invert the palette direction
in the Black & White visualization mode (see Black & White Mode).
This command only is enabled if the active visualization mode is Black & White.
Use Maximum
This command appears in the View menu. It works as a toggle, when not active the action
in the commands Show Maximum and Plot Maximum in sequence is inverted becoming
Show Minimum and Plot Minimum in sequence. The work sheet Max. Intensity Projection
becomes Min. Intensity Projection also, plotting in this case only the values with the
minimum intensity.
Invert MIP back.
This command appears in the View menu. It works as a toggle, when not active the image
background in the sheet Maximun/Minimun Intensity Projection is plotted in black. When
active the background is inverted and becomes white.
Isocontour style
This command in the View menu sets the way in which the isocontours are plotted (see
Isocontour Mode). By means of an edit box it is possible to set the step between an
isocontour and the next one. When the step is small the the isocontours will cover more of
the image and viceversa.
Figure 44. Dialog for Isocontour style.
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Description of comnands
Slice orientation
This command in the View menu brings up a dialog window to selecting the orientation of
the slices in each plane appears.
Figure 45. Slice orientation dialog.
Plane in All Slices
This command in the View menu opens a dialog window to select which orthogonal plane
will be shown in the All Slices work sheet (see All Slices).
All Slices Reference
This command in the View menbrings up the auxiliary reference window in the All Slices
work sheet (see All Slices).
Contents
This command in the Help menu opens the BET Viewer help system using the standard
Windows help system.
The shortcut key F1 provides help specific to some windows in the application.
Keyword Search
This command in the Help menuopens the BET Viewer help system for keyword search
using the standard Windows help system.
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Using Help
This command in the Help menu opens the standard Windows help system explanations.
About
This command in the Help menu shows information about the application.
What's This ?
This command appears in the local menus of the work sheets 3D View and Electrode View.
When activated, a window shows the parameters used for the rendering on which the
mouse cursor is located when it was carried out. The window can be closed by pressing the
left button mouse or the Esc key.
Figure 46. Parameters report for the rendering 3D.
Clear this
This command in the local menus of the work sheets 3D View and Electrode View deletes
the rendering on which the mouse cursor was located. For deleting all the renderings the
command Clear all should be used.
Show Identifiers
This toggle command in the local menu of the Electrode View work sheet shows the names
of the visible electrodes.
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